20-6636225-G-T

Variant names:

• chr20-6636225-G-T
• rs1407027

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.154 in 152,090 control chromosomes in the GnomAD database, including 2,009 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.15 (2009 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.723
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.187 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.154 AC: 23424 AN: 151972 Hom.: 2007 Cov.: 32

Gnomad AFR AF: 0.0867

Gnomad AMI AF: 0.182

Gnomad AMR AF: 0.189

Gnomad ASJ AF: 0.166

Gnomad EAS AF: 0.0608

Gnomad SAS AF: 0.197

Gnomad FIN AF: 0.159

Gnomad MID AF: 0.165

Gnomad NFE AF: 0.189

Gnomad OTH AF: 0.159

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.154 AC: 23434 AN: 152090 Hom.: 2009 Cov.: 32 AF XY: 0.152 AC XY: 11336 AN XY: 74342

African (AFR) AF: 0.0869 AC: 3606 AN: 41500

American (AMR) AF: 0.189 AC: 2879 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.166 AC: 575 AN: 3468

East Asian (EAS) AF: 0.0608 AC: 314 AN: 5168

South Asian (SAS) AF: 0.198 AC: 953 AN: 4818

European-Finnish (FIN) AF: 0.159 AC: 1685 AN: 10584

Middle Eastern (MID) AF: 0.150 AC: 44 AN: 294

European-Non Finnish (NFE) AF: 0.189 AC: 12881 AN: 67974

Other (OTH) AF: 0.157 AC: 332 AN: 2112

Alfa AF: 0.0870 Hom.: 137

Bravo AF: 0.153

Asia WGS AF: 0.125 AC: 435 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.49
DANN	Benign	0.27
PhyloP100		-0.72

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs1407027; hg19: chr20-6616872;